Search found 29 matches

by sbrich
Tue Mar 17, 2020 11:31 am
Forum: OS X
Topic: NRNGUI not working from command line after switch to zsh
Replies: 10
Views: 2348

Re: NRNGUI not working from command line after switch to zsh

Zsh has two things that are roughly equivalent to .bashrc (and .bash_profile): .zshrc and .zshenv (both of these files go in your home folder; they may or may not already be there). .zshrc is only used by interactive shells, and .zshenv is used by all shells, interactive or not. Thus you probably w...
by sbrich
Tue Mar 17, 2020 10:30 am
Forum: OS X
Topic: NRNGUI not working from command line after switch to zsh
Replies: 10
Views: 2348

Re: NRNGUI not working from command line after switch to zsh

Zsh has two things that are roughly equivalent to .bashrc (and .bash_profile): .zshrc and .zshenv (both of these files go in your home folder; they may or may not already be there). .zshrc is only used by interactive shells, and .zshenv is used by all shells, interactive or not. Thus you probably w...
by sbrich
Fri Mar 13, 2020 3:24 pm
Forum: OS X
Topic: NRNGUI not working from command line after switch to zsh
Replies: 10
Views: 2348

NRNGUI not working from command line after switch to zsh

Hello all, I've been preparing to embark upon a new project, learning Python (finally!). In preparation for this I had to do some tweaks to my Terminal in Mac, including switching from the old "bash" to the new "zsh" terminal (whatever that means!). Now, all my Python, anaconda, ...
by sbrich
Thu Nov 21, 2019 1:37 pm
Forum: OS X
Topic: NEURON not working properly after update to Catalina and major troubleshooting!
Replies: 3
Views: 1874

Re: NEURON not working properly after update to Catalina and major troubleshooting!

Not related to the problem that triggered this thread, but something you need to know: for your ODE-described calcium accumulation mechanism, use derivimplicit rather than cnexp. See Integration methods for SOLVE statements https://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592 in the Hot t...
by sbrich
Thu Nov 21, 2019 1:01 pm
Forum: OS X
Topic: NEURON not working properly after update to Catalina and major troubleshooting!
Replies: 3
Views: 1874

Re: NEURON not working properly after update to Catalina and major troubleshooting!

OK, so as always seems to be the case when it comes to tech troubleshooting, I seem to have made some progress after posting this. I reran nrnivmodl and tried again, and got a new error message: Mechanism CaDynamics_E2 needs to be re-translated. It's version 7.5.0 "c" code is incompatible ...
by sbrich
Thu Nov 21, 2019 12:36 pm
Forum: OS X
Topic: NEURON not working properly after update to Catalina and major troubleshooting!
Replies: 3
Views: 1874

NEURON not working properly after update to Catalina and major troubleshooting!

Hello all, I am experiencing a very odd issue with NEURON after updating my Macbook Pro to the newest OS (Catalina). At first, it appeared that something was awry with Python, so I went through a long and arduous process of uninstalling and reinstalling Anaconda (both versions 2 and 3). When this di...
by sbrich
Tue May 07, 2019 4:21 pm
Forum: Anatomically detailed models
Topic: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)
Replies: 3
Views: 1925

Re: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)

Everything worked perfectly... thanks for the help Ted, and my apologies again for overlooking what was a very straightforward solution!
by sbrich
Mon May 06, 2019 10:06 am
Forum: Anatomically detailed models
Topic: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)
Replies: 3
Views: 1925

Re: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)

Thank you very much Ted! My apologies for the confusion on what ended up being a somewhat trivial question: as I alluded to, the morphology was the one part of this project that I was not directly involved with, as it was done before I joined my lab. Unfortunately the former lab member who was in ch...
by sbrich
Fri May 03, 2019 10:46 am
Forum: Anatomically detailed models
Topic: Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)
Replies: 3
Views: 1925

Recreating JUST the morphology from an available model (that is coded in an unfamiliar way)

Hello NEURON forums, My continuing work on a detailed multi-compartment neuron model (that I've already posted quite a few questions on these forums regarding, haha) is nearing it's conclusion! We have a model that we're very happy with up and running, and we're now doing some in silico experiments ...
by sbrich
Tue Mar 12, 2019 1:25 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 3996

Re: Confusion regarding get_loc and h.cas

I think we're talking about different things here... let me try and rephrase. I agree with your comment regarding Lists, and am forgetting entirely about everything I wrote pre-Lists. Now everything I'm using is in List form. My synapses are located correctly based on every check I've been able to p...
by sbrich
Tue Mar 12, 2019 1:11 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 3996

Re: Confusion regarding get_loc and h.cas

Hi Ted, Happy to report that using Lists and the function you provided solved my problem... for the most part. I'm still curious about one, minor issue (more for my own edification and improving my overall understanding of NEURON than anything else). As it stands, now that everything is a list, when...
by sbrich
Tue Mar 12, 2019 12:41 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 3996

Re: Confusion regarding get_loc and h.cas

OK, I think this is starting to make more sense now. I'll go back into my code and redo things with lists as opposed to the N objrefs I was using previously, and then see if I'm able to recover the section info. Here's what I'm still confused about: even if using N objrefs as I was previously doing ...
by sbrich
Tue Mar 12, 2019 10:36 am
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 3996

Re: Confusion regarding get_loc and h.cas

Thanks Ted. One last question here. I think I'm doing something similar to what you're suggesting in my code already: namely, since I'm creating a large number of synapses, I use a single object to store them all in. Namely: numsyn=1000 // Number of synapses I'm creating in this run ... objref spike...
by sbrich
Mon Mar 11, 2019 3:30 pm
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 3996

Re: Confusion regarding get_loc and h.cas

Thanks Ted... I figured I was confused on something low-level, but didn't realize how confused, haha. To answer your question, I'm only using hoc syntax (I don't know Python... learning it has long been on my ever growing to-do list!). I believe I remember seeing that the h.cas was Python based, but...
by sbrich
Mon Mar 11, 2019 10:35 am
Forum: Anatomically detailed models
Topic: Confusion regarding get_loc and h.cas
Replies: 11
Views: 3996

Re: Confusion regarding get_loc and h.cas

My apologies for the "double post", but was curious to see if anyone could help me with this issue. Thanks!